Methods for detecting interaction between a test moiety and a plurality of target moieties

ABSTRACT

This invention relates generally to the field of microarray technology. In particular, the invention provides an integrated microarray device, which device comprises a substrate comprising a plurality of distinct microlocations and a plurality of microarray chips, wherein the number of said microlocations equals to or is more than the number of said microarray chips. In preferred embodiments, the devices also comprises a temperature controller at some or all of the microlocations. The use of the integrated microarray devices for detecting interactions among various moieties in various fields, such as clinical diagnostics, drug discovery, environmental monitoring and forensic analysis, etc., are further provided.

RELATED APPLICATION

[0001] This application is related to a Chinese national patentapplication Serial No. 00109792.X, filed Jul. 4, 2000, entitled“INTEGRATED MICROARRAY DEVICES.”

[0002] The disclosure of the above referenced patent application isincorporated by reference in their entirety.

TECHNICAL FIELD

[0003] This invention relates generally to the field of microarraytechnology. In particular, the invention provides an integratedmicroarray device, which device comprises a substrate comprising aplurality of distinct microlocations and a plurality of microarraychips, wherein the number of said microlocations equals to or is morethan the number of said microarray chips. In preferred embodiments, thedevices also comprise a temperature controller at some or all of themicrolocations. The use of the integrated microarray devices fordetecting interactions among various moieties in various fields, such asclinical diagnostics, drug discovery, environmental monitoring andforensic analysis, etc., are further provided.

BACKGROUND ART

[0004] Microarray technology has been developing quickly since it firstappeared in the 1990's (Fodor et al., Science, 251:767-773 (1991)). Nowas a representative category of biochip technology, microarraytechnology has been widely utilized in clinical diagnostics, diseasemechanism research, drug discovery, environmental monitoring, functionalgenomics research etc. (Hacia et al., Nature Genetics, 14: 441-447(1996); and Heller et al., Proc. Natl. Acad. Sci. USA, 94: 2150-2155(1997)). Biological probes, such as oligonucleotides, DNA, RNA,peptides, proteins, cells, tissues, are immobilized on the surface ofvarious substrate such as glass, silicon, nylon membrane etc. Theseprobes represent particular information respectively. Sample is addedinto the reaction well in which the microarray is put to interact withimmobilized probes. Sample may be labeled by isotope, fluorescentreagents, chemiluminescent reagents to facilitate the detection.

[0005] According to different labeling methods, various detectionmethods can be used, such as confocal fluorescent scanner, lowluminescence detector, isotope imager, etc.

[0006] To achieve high-throughput parallel analysis, high densitymicroarrays have been developed on which several hundred thousand probesare immobilized. But in many cases, high density and high costmicroarrays are not absolutely necessary. Moreover, high densitymicroarrays do not necessarily mean high fidelity of detection signalbecause different probes on the microarray have subtle distinctions bynature. For example, if probes are DNA molecules, they may havedifferent number of bases or different sequences, both of whichcontribute to the consequence of varied optimal hybridizationconditions. Only under optimal hybridization conditions, mismatch ratiocan be reduced to low level to facilitate the generation of accuratehybridization signals.

[0007] Furthermore, the detection operation is inconvenient for mostmicroarrays as they must be detected one at a time.

DISCLOSURE OF THE INVENTION

[0008] This invention provides an integrated microarray device which canbe applied to multiple chemical and/or biological sample reactions anddetections with high efficiency, high fidelity and low cost.

[0009] In one aspect, the invention provides an integrated microarraydevice, which device comprises a substrate comprising a plurality ofdistinct microlocations and a plurality of microarray chips, wherein thenumber of said microlocations equals to or is more than the number ofsaid microarray chips. In preferred embodiments, the devices alsocomprise a temperature controller at some or all of the microlocations.

[0010] In another aspect, the invention provides a method for detectinginteraction between a test moiety and a plurality of target moieties,which method comprises: a) providing an integrated microarray device,which device comprises a substrate comprising a plurality of distinctmicrolocations and a plurality of microarray chips, wherein the numberof said microlocations equals to or is more than the number of saidmicroarray chips, and a plurality of target moieties attached to saidmicroarray chips; b) contacting a test moiety with said plurality oftarget moieties provided in step a); and c) detecting interactionbetween said test moiety and said plurality of target moieties.

[0011] In a preferred embodiment, the device provided herein includes asubstrate, on which reaction wells are fabricated. In every reactionwell a microarray chip is placed in. This microarray chip may be of ahigh, or low, preferably, a low density chip. In addition, a temperaturecontroller is placed inside or outside every reaction well mentionedabove. These temperature controllers can individually control thetemperature in each reaction well. When fabricating microarray chipscustomarily made for such microarray device, probes are divided intodifferent groups according to their respective melting temperatures(T_(m) value). Probes with close enough melting temperature values areimmobilized on one microarray chip; the chip is then put into onereaction well. Reaction temperature in different reaction well can becontrolled individually by attached temperature controller. The reactiontemperature in every well can be controlled exactly according to theT_(m) value of probes immobilized so that false positive rate ordetection error caused by the inappropriate temperature control can bereduced. The dimension of this microarray device corresponds to standard96-well plate, 384-well plate or 1536-well plate. That is, the number ofreaction wells and the distance between different wells arestandardized. This design facilitates simple, high efficient andautomatic manipulation such as sample handling and washing by robotics.

BRIEF DESCRIPTION OF THE DRAWINGS

[0012] In the drawings, the same reference numbers represent the sameparts.

[0013]FIG. 1 is the top-view schematic illustration of an exemplaryintegrated microarray device.

[0014]FIG. 2 is the three-dimensional schematic illustration of one unitin an exemplary integrated microarray device.

[0015]FIG. 3 schematically illustrates the electronic connection linesof the temperature controllers, as parts of an exemplary integratedmicroarray device.

[0016]FIG. 4 is the structure schematic illustration of a semiconductortemperature controller used for microarray device of this invention.

MODES OF CARRYING OUT THE INVENTION

[0017] For clarity of disclosure, and not by way of limitation, thedetailed description f the invention is divided into the subsectionsthat follow.

[0018] A. Definitions

[0019] Unless defined otherwise, all technical and scientific terms usedherein have the same meaning as is commonly understood by one ofordinary skill in the art to which this invention belongs. All patents,applications, published applications and other publications referred toherein are incorporated by reference in their entirety. If a definitionset forth in this section is contrary to or otherwise inconsistent witha definition set forth in applications, published applications and otherpublications that are herein incorporated by reference, the definitionset forth in this section prevails over the definition that isincorporated herein by reference.

[0020] As used herein, “a” or “an” means “at least one” or “one ormore.”

[0021] As used herein, “microarray chip” refers to a solid substratewith a plurality of one-, two- or three-dimensional micro structures ormicro-scale structures on which certain processes, such as physical,chemical, biological, biophysical or biochemical processes, etc., can becarried out. The micro structures or micro-scale structures such as,channels and wells, are incorporated into, fabricated on or otherwiseattached to the substrate for facilitating physical, biophysical,biological, biochemical, chemical reactions or processes on the chip.The chip may be thin in one dimension and may have various shapes inother dimensions, for example, a rectangle, a circle, an ellipse, orother irregular shapes. The size of the major surface of chips can varyconsiderably, e.g., from about 1 mm² to about 0.25 m². Preferably, thesize of the chips is from about 4 mm² to about 25 cm² with acharacteristic dimension from about 1 mm to about 5 cm. The chipsurfaces may be flat, or not flat. The chips with non-flat surfaces mayinclude channels or wells fabricated on the surfaces.

[0022] As used herein, “microlocations” refers to places that arewithin, on the surface or attached to the substrate wherein themicroarray chips and/or other structures or devices are located.

[0023] As used herein, “distinct microlocations” means that themicrolocations are sufficiently separated so that, if needed, reagentscan be added and/or withdrawn and reactions can be conducted in onemicrolocation independently from another microlocation. It is notnecessary that each microlocation is “distinct” from all othermicrolocations, although in certain embodiments, each microlocation canbe “distinct” from all other microlocations.

[0024] As used herein, “microlocations are in a well format” means thatthere are indentations with suitable three dimensional shape at themicrolocations so that microarray chips and/or other structures ordevices such as temperature controllers, can be built or placed into.

[0025] As used herein, “microlocations is thermally insulated” meansthat the microlocations have certain structures or substances that canbe used to adjust to and maintain temperature at a microlocation at adesired level independently from other microlocations or any placeoutside the microlocation.

[0026] As used herein, “moiety” encompasses both test moiety and targetmoiety. Non-limiting examples of moieties include cells, cellularorganelles, viruses, particles, molecules, e.g., proteins, DNAs andRNAs, or an aggregate or complex thereof.

[0027] As used herein, “plant” refers to any of various photosynthetic,eucaryotic multi-cellular organisms of the kingdom Plantae,characteristically producing embryos, containing chloroplasts, havingcellulose cell walls and lacking locomotion.

[0028] As used herein, “animal” refers to a multi-cellular organism ofthe kingdom of Animalia, characterized by a capacity for locomotion,nonphotosynthetic metabolism, pronounced response to stimuli, restrictedgrowth and fixed bodily structure. Nonlimiting examples of animalsinclude birds such as chickens, vertebrates such fish and mammals suchas mice, rats, rabbits, cats, dogs, pigs, cows, ox, sheep, goats,horses, monkeys and other non-human primates.

[0029] As used herein, “bacteria” refers to small prokaryotic organisms(linear dimensions of around 1 micron) with non-compartmentalizedcircular DNA and ribosomes of about 70S. Bacteria protein synthesisdiffers from that of eukaryotes. Many anti-bacterial antibioticsinterfere with bacteria proteins synthesis but do not affect theinfected host.

[0030] As used herein, “eubacteria” refers to a major subdivision of thebacteria except the archaebacteria. Most Gram-positive bacteria,cyanobacteria, mycoplasmas, enterobacteria, pseudomonas and chloroplastsare eubacteria. The cytoplasmic membrane of eubacteria containsester-linked lipids; there is peptidoglycan in the cell wall (ifpresent); and no introns have been discovered in eubacteria.

[0031] As used herein, “archaebacteria” refers to a major subdivision ofthe bacteria except the eubacteria. There are three main orders ofarchaebacteria: extreme halophiles, methanogens and sulphur-dependentextreme thermophiles. Archaebacteria differs from eubacteria inribosomal structure, the possession (in some case) of introns, and otherfeatures including membrane composition.

[0032] As used herein, “virus” refers to an obligate intracellularparasite of living but non-cellular nature, consisting of DNA or RNA anda protein coat. Viruses range in diameter from about 20 to about 300 nm.Class I viruses (Baltimore classification) have a double-stranded DNA astheir genome; Class II viruses have a single-stranded DNA as theirgenome; Class III viruses have a double-stranded RNA as their genome;Class IV viruses have a positive single-stranded RNA as their genome,the genome itself acting as mRNA; Class V viruses have a negativesingle-stranded RNA as their genome used as a template for mRNAsynthesis; and Class VI viruses have a positive single-stranded RNAgenome but with a DNA intermediate not only in replication but also inmRNA synthesis. The majority of viruses are recognized by the diseasesthey cause in plants, animals and prokaryotes. Viruses of prokaryotesare known as bacteriophages.

[0033] As used herein, “fungus” refers to a division of eucaryoticorganisms that grow in irregular masses, without roots, stems, orleaves, and are devoid of chlorophyll or other pigments capable ofphotosynthesis. Each organism (thallus) is unicellular to filamentous,and possesses branched somatic structures (hyphae) surrounded by cellwalls containing glucan or chitin or both, and containing true nuclei.

[0034] As used herein, “intracellular moiety” refers to any moiety thatresides or is otherwise located within a cell, i.e., located in thecytoplasm or matrix of cellular organelle, attached to any intracellularmembrane, resides or is otherwise located within periplasma, if there isone, or resides or is otherwise located on cell surface, i.e., attachedon the outer surface of cytoplasm membrane or cell wall, if there isone.

[0035] As used herein, “macromolecule” refers to a molecule that,without attaching to another molecule, is capable of generating anantibody that specifically binds to the macromolecule.

[0036] As used herein, “small molecule” refers to a molecule that,without forming homo-aggregates or without attaching to a macromoleculeor adjuvant, is incapable of generating an antibody that specificallybinds to the small molecule. Preferably, the small molecule has amolecular weight that is about or less than 10,000 daltons. Morepreferably, the small molecule has a molecular weight that is about orless than 5,000 dalton.

[0037] As used herein, “vitamin” refers to a trace organic substancerequired in certain biological species. Most vitamins function ascomponents of certain coenzymes.

[0038] As used herein, “lipid” refers to water-insoluble, oily or greasyorganic substances that are extractable from cells and tissues bynonpolar solvents, such as chloroform or ether.

[0039] As used herein, a “receptor” refers to a molecule that has anaffinity for a given ligand. Receptors may be naturally-occurring orsynthetic molecules. Receptors may also be referred to in the art asanti-ligands. As used herein, the receptor and anti-ligand areinterchangeable. Receptors can be used in their unaltered state or asaggregates with other species. Receptors may be attached, covalently ornoncovalently, or in physical contact with, to a binding member, eitherdirectly or indirectly via a specific binding substance or linker.Examples of receptors, include, but are not limited to: antibodies, cellmembrane receptors surface receptors and internalizing receptors,monoclonal antibodies and antisera reactive with specific antigenicdeterminants [such as on viruses, cells, or other materials], drugs,polynucleotides, nucleic acids, peptides, cofactors, lectins, sugars,polysaccharides, cells, cellular membranes, and organelles.

[0040] As used herein, “antibody” includes antibody fragments, such asFab fragments, which are composed of a light chain and the variableregion of a heavy chain.

[0041] As used herein, “humanized antibodies” refer to antibodies thatare modified to include “human” sequences of amino acids so thatadministration to a human will not provoke an immune response. Methodsfor preparation of such antibodies are known. For example, the hybridomathat expresses the monoclonal antibody is altered by recombinant DNAtechniques to express an antibody in which the amino acid composition ofthe non-variable regions is based on human antibodies. Computer programshave been designed to identify such regions.

[0042] As used herein, “a group of structurally and/or functionallyrelated proteins” refers to a group of proteins, at their naturalstatus, that are structurally linked, located at the same cellularlocations, e.g., cellular organelles, located in the same tissues ororgans, expressed and/or be functional in the same biological stages,e.g., a particular cell cycle stage or developmental stage, or expressedand/or be functional in the same biological pathway, e.g., a particularmetabolism pathway, signal transduction pathway, etc. The “group ofstructurally and/or functionally related proteins” need only include atleast two proteins belonging to the same group. The “group ofstructurally and/or functionally related proteins” can preferablyinclude more than two proteins belonging to the same group, e.g., amajority of or even all the proteins belonging to the same group.

[0043] As used herein, “nutrient or storage protein” refers to a proteinthat is used by the cell as the nutrient source or storage form for suchnutrient. Non-limiting examples of nutrient or storage proteins includegliadin, ovalburnin, casein, and ferritin.

[0044] As used herein, “contractile or motile protein” refers to aprotein that endows cells and organisms with the ability to contract, tochange shape, or to move about. Nonlimiting examples of contractile ormotile proteins include actin, myosin, tubulin and dynein.

[0045] As used herein, “structural protein” refers to a protein thatserves as supporting filaments, cables, or sheets to give biologicalstructures strength or protection. Nonlimiting examples of structuralproteins include keratin, fibroin, collagen, elastin and proteoglycans.

[0046] As used herein, “defense protein” refers to a protein thatdefends organisms against invasion by other species or protect them frominjury. Non-limiting examples of defense proteins include antibodies,fibrinogen, thrombin, botulinus toxin, diphtheria toxin, snake venomsand ricin.

[0047] As used herein, “regulatory protein” refers to a protein thathelps regulate cellular or physiological activity. Non-limiting examplesof regulatory proteins include insulin, growth hormones, corticotropinand repressors.

[0048] As used herein, “sample” refers to anything which may contain ananalyte for which an analyte assay is desired. The sample may be abiological sanple, such as a biological fluid or a biological tissue.Examples of biological fluids include urine, blood, plasma, serum,saliva, semen, stool, sputum, cerebral spinal fluid, tears, mucus,amniotic fluid or the like. Biological tissues are aggregates of cells,usually of a particular kind together with their intercellular substancethat form one of the structural materials of a human, animal, plant,bacterial, fungal or viral structure, including connective, epithelium,muscle and nerve tissues. Examples of biological tissues also includeorgans, tumors, lymph nodes, arteries and individual cell(s). The samplemay also be a mixture of target protein containing molecules prepared invitro.

[0049] As used herein, “a group of structurally and/or functionallyrelated enzymes” refers to a group of enzymes, at their natural status,that are structurally linked, located at the same cellular locations,e.g., cellular organelles, located in the same tissues or organs,expressed and/or be functional in the same biological stages, e.g., aparticular cell cycle stage or developmental stage, or expressed and/orbe functional in the same biological pathway, e.g., a particularmetabolism pathway, signal transduction pathway, or act as a regulatorfor a pathway activation or a biological function, etc. The “group ofstructurally and/or functionally related enzymes” need only include atleast two enzymes belonging to the same group. The “group ofstructurally and/or functionally related enzymes” can preferably includemore than two enzymes belonging to the same group, e.g., a majority ofor even all the enzymes belonging to the same group.

[0050] As used herein, “expressed in a tissue or organ specific manner”refers to a gene expression pattern in which a gene is expressed, eithertransiently or constitutively, only in certain tissues or organs, butnot in other tissues or organs.

[0051] As used herein, “tissue” refers to a collection of similar cellsand the intracellular substances surrounding them. There are four basictissues in the body: 1) epithelium; 2) connective tissues, includingblood, bone, and cartilage; 3) muscle tissue; and 4) nerve tissue.

[0052] As used herein, “organ” refers to any part of the body exercisinga specific function, as of respiration, secretion or digestion.

[0053] As used herein: “stringency of hybridization” in determiningpercentage mismatch is as follows:

[0054] 1) high stringency: 0.1× SSPE, 0.1% SDS, 65° C.;

[0055] 2) medium stringency: 0.2× SSPE, 0.1% SDS, 50° C. (also referredto as moderate stringency); and

[0056] 3) low stringency: 1.0× SSPE, 0.1% SDS, 50° C.

[0057] It is understood that equivalent stringencies may be achievedusing alternative buffers, salts and temperatures.

[0058] As used herein, “gene” refers to the unit of inheritance thatoccupies a specific locus on a chromosome, the existence of which can beconfirmed by the occurrence of different allelic forms. Given theoccurrence of split genes, gene also encompasses the set of DNAsequences (exons) that are required to produce a single polypeptide.

[0059] As used herein, “gene chip” refers to an array ofoligonucleotides immobilized on a surface that can be used to screen anRNA sample (after reverse transcription) and thus a method for rapidlydetermining which genes are being expressed in the cell or tissue fromwhich the RNA came.

[0060] As used herein, “RNA” refers to ribose units joined in the 3′ and5′ positions through a phosphodiester linkage with a purine orpyrimidine base attached to the 1′ position.

[0061] As used herein, “protein” refers to a linear polymer of aminoacids joined by peptide bonds in a specific sequence. As used herein,“protein” also encompasses polypeptide, oligopeptide and peptide.

[0062] B. Integrated Microarray Devices

[0063] In one aspect, the invention provides an integrated microarraydevice, which device comprises a substrate comprising a plurality ofdistinct microlocations and a plurality of microarray chips, wherein thenumber of said microlocations equals to or is more than the number ofsaid microarray chips.

[0064] Any suitable substrate can be used in the present integratedmicroarray device. In a preferred embodiment, the substrate comprisessilicon, e.g., silicon dioxide or silicon nitride, plastic, glass,ceramic, rubber, polymer or a composite thereof. The substrate cancomprise a surface that is hydrophobic or hydrophilic. In addition, thesubstrate can comprise a surface that is porous or nonporous.

[0065] The microlocations can be made within, on or attached to thesubstrate by any suitable methods. For example, the microlocations canbe produced directly as part of the substrate. Alternatively, thesubstrate can be produced first and the microlocations are subsequentlybe made within, on or attached to the substrate. In a preferredembodiment, the microlocations and/or the microarray chips arefabricated on the substrate. The device can comprise any suitable numberof microlocations. For example, the device can comprise (12)_(n) numberof microlocations, wherein n is an integer that is at least 1.Preferably, n is 8, 32 or 128. The microlocations can be evenly orunevenly distributed on the substrate. Preferably, the numbermicrolocations and the distance among the microlocations correspond to astandard microtiter plate, e.g., 96-, 384-, or 1536-well plate.

[0066] The microlocations can be in any suitable format. For example,the microlocations can be made within the substrate or can be made onthe surface or above the surface of the substrate. Preferably, themicrolocations are in a well format or a thermally insulated flatsurface format. The device can comprise (12)_(n) number of wells,wherein n is an integer that is at least 1. Preferably, the devicecomprises 96, 384 or 1,536 wells. The wells can have any suitable threedimensional shapes or geometries. For example, the top, middle and/orbottom portion of the wells can be circle, oval, square, rectangle,triangle and other irregular shape(s). The top, middle and/or bottomportion of the wells can have the same or different shapes and/or areas.The device can comprise wells having identical or differenttwo-dimensional or three-dimensional shapes or geometries.

[0067] The microlocations can be in fluid contact with a fluid source orfluid passage outside the device. Any number or percentage of themicrolocations, e.g., 50% of the microlocations, can be in fluid contactwith a fluid source or fluid passage outside the device. Preferably, allof the microlocations are in fluid contact with a fluid source or fluidpassage outside the device. In a specific embodiment, at least two ofthe microlocations can be in fluid contact with each other. Any numberor percentage of the microlocations, e.g., 50% of the microlocations,can be in fluid contact with each other. Preferably, all of themicrolocations are in fluid contact with each other. The microlocationscan be made in fluid contact with a fluid source or fluid passageoutside the device and/or with each other using any suitable structures,e.g., microfluidic channels.

[0068] In a specific embodiment, at least one of the microlocations,e.g., wells, can be thermally insulated. Any number or percentage of themicrolocations, e.g., 50% of the microlocations, can be thermallyinsulated. Preferably, all of the microlocations can be thermallyinsulated. The microlocations can be thermally insulated using anysuitable structures or materials. For example, the microlocation(s) canbe thermally insulated by inert gas, e.g., air. In a preferredembodiment, some wells or all of the wells are connected to each otherby thin girders and thermally insulated by the air contained between thewalls of the adjacent wells.

[0069] The number of the microlocations in the present device should bemore than or equal to the number of the microarray chips. Preferably,each of the microlocations in the device comprises a microarray chip.

[0070] Any suitable microarray chips can be used in the presentintegrated microarray device. For example, microarray chips suitable fornucleic acid analysis, e.g., gene chip, and/or protein chip, antibodychip, can be used in the present device (See generally, Ausubel et al.,Current Protocols in Molecular Biology, §22, John Wiley & Sons, Inc.(2000); and Schena (Ed.), Microarray Biochip technology, EatonPublishing Company/Bio Techniques Books Division (2000)). In a specificembodiment, the microarray chips disclosed in the following U.S. Pat.Nos. can be used in the present device: U.S. Pat. Nos. 6,245,511,6,215,894, 6,142,681, 6,101,946, 6,004,755, 5,930,117, 5,928,437 and5,716,459.

[0071] The microarray chips can have any desirable densities. Themicroarray chips can have identical or different densities. In aspecific embodiment, the microarray chips have a density of (100)_(n)spots/cm², wherein n is an integer that is at least 1. Preferably, atleast one of the microarray chips has a density that is less than orequals to 400 spots/cm². However, any number or percentage of themicroarray chips, e.g., 50% of the microarray chips, can have a densitythat is less than or equals to 400 spots/cm². More preferably, all ofthe microarray chips have a density that is less than or equals to 400spots/cm².

[0072] In another specific embodiment, at least one of the microarraychips has attached thereto a plurality of moieties. The microarraychip(s) can have attached thereto a plurality of moieties on facing upor down direction. The moieties can be attached to the microarraychip(s) using any suitable methods. The moieties can be attached to themicroarray chip(s) covalently, non-covalently, through specific ornon-specific linkage, can be attached directly or through a linker. Thelinker can be sensitive to certain treatment, such as physical, chemicalor enzymatic treatment.

[0073] Any suitable moieties can be attached to the microarray chip(s).The moieties can be pure substances or composite materials, can bechemical or biological materials, or can be synthetic orisolated/purified from biological sources or samples. Exemplary moietiesinclude cells, cellular organelles, viruses, molecules and an aggregateor complex thereof.

[0074] Non-limiting examples of cells include animal, plant, fungi,bacteria, recombinant or cultured cells. Animal, plant, fungus,bacterium cells can be derived from any genus or subgenus of theAnimalia, Plantae, fungus or bacterium kingdom. Cells derived from anygenus or subgenus of ciliates, cellular slime molds, flagellates andmicrosporidia can also be attached to the microarray chip(s). Cellsderived from birds such as chickens, vertebrates such as fish andmammals such as mice, rats, rabbits, cats, dogs, pigs, cows, ox, sheep,goats, horses, monkeys and other non-human primates, and humans can beattached to the microarray chip(s).

[0075] For animal cells, cells derived from a particular tissue or organcan be attached to the microarray chip(s). For example, connective,epithelium, muscle or nerve tissue cells can be used. Similarly, cellsderived from an accessory organ of the eye, annulospiral organ, auditoryorgan, Chievitz organ, circumventricular organ, Corti organ, criticalorgan, enamel organ, end organ, external female gential organ, externalmale genital organ, floating organ, flower-spray organ of Ruffini,genital organ, Golgi tendon organ, gustatory organ, organ of hearing,internal female genital organ, internal male genital organ, intromittentorgan, Jacobson organ, neurohemal organ, neurotendinous organ, olfactoryorgan, otolithic organ, ptotic organ, organ of Rosenmüller, sense organ,organ of smell, spiral organ, subcommissural organ, subformical organ,supernumerary organ, tactile organ, target organ, organ of taste, organof touch, urinary organ, vascular organ of lamina terminalis, vestibularorgan, vestibulocochlear organ, vestigial organ, organ of vision, visualorgan, vomeronasal organ, wandering organ, Weber organ and organ ofZuckerkandl can be used. Preferably, cells derived from an internalanimal organ such as brain, lung, liver, spleen, bone marrow, thymus,heart, lymph, blood, bone, cartilage, pancreas, kidney, gall bladder,stomach, intestine, testis, ovary, uterus, rectum, nervous system,gland, internal blood vessels, etc can be used. Further, cells derivedfrom any plants, fungi such as yeasts, bacteria such as eubacteria orarchaebacteria can be used. Recombinant cells derived from anyeucaryotic or prokaryotic sources such as animal, plant, fungus orbacterium cells can also be used. Body fluid such as blood, urine,saliva, bone marrow, sperm or other ascitic fluids, and subfractionsthereof, e.g., serum or plasma, can also be used.

[0076] Attachable cellular organelles include nucleus, mitochondria,chloroplasts, ribosomes, ERs, Golgi apparatuses, lysosomes, proteasomes,secretory vesicles, vacuoles or microsomes. Attachable viruses, whetherintact viruses or any viral structures, e.g., viral particles, in thevirus life cycle can be derived from viruses such as Class I viruses,Class II viruses, Class III viruses, Class IV viruses, Class V virusesor Class VI viruses.

[0077] Attachable intracellular moiety include any moiety that residesor is otherwise located within a cell, i.e., located in the cytoplasm ormatrix of cellular organelle; attached to any intracellular membrane;resides or is otherwise located within periplasma, if there is one; orresides or is otherwise located on cell surface, i.e., attached on theouter surface of cytoplasm membrane or cell wall, if there is one. Anydesired intracellular moiety can be isolated from the target cell(s).For example, cellular organelles, molecules or an aggregate or complexthereof can be isolated. Non-limiting examples of such cellularorganelles include nucleus, mitochondria, chloroplasts, ribosomes, ERs,Golgi apparatuses, lysosomes, proteasomes, secretory vesicles, vacuolesor microsomes, membrane receptors, antigens, enzymes and proteins incytoplasm.

[0078] Attachable molecules can be inorganic molecules such as ions,organic molecules or a complex thereof. Non-limiting examples ofattachable ions include sodium, potassium, magnesium, calcium, chlorine,iron, copper, zinc, manganese, cobalt, iodine, molybdenum, vanadium,nickel, chromium, fluorine, silicon, tin, boron or arsenic ions.Non-limiting examples of attachable organic molecules include aminoacids, peptides, proteins, nucleosides, nucleotides, oligonucleotides,nucleic acids, vitamins, monosaccharides, oligosaccharides,carbohydrates, lipids or a complex thereof.

[0079] Any amino acids can be attached to the microarray chip(s). Forexample, a D- and a L-amino-acid can be attached. In addition, anybuilding blocks of naturally occurring peptides and proteins includingAla (A), Arg (R), Asn (N), Asp (D), Cys (C), Gln (Q), Glu (E), Gly (G),His (H), Ile (I), Leu (L), Lys (K), Met (M), Phe (F), Pro (P) Ser (S),Thr (T), Trp (W), Tyr (Y) and Val (V) can be attached.

[0080] Any proteins or peptides can be attached to the microarraychip(s). For example, enzymes, transport proteins such as ion channelsand pumps, nutrient or storage proteins, contractile or motile proteinssuch as actins and myosins, structural proteins, defense protein orregulatory proteins such as antibodies, hormones and growth factors canbe attached. Proteineous or peptidic antigens can also be attached.

[0081] Any nucleic acids, including single-, double and triple-strandednucleic acids, can be attached to the microarray chip(s). Examples ofsuch nucleic acids include DNA, such as A-, B- or Z-form DNA, and RNAsuch as mRNA, tRNA and rRNA.

[0082] Any nucleosides can be attached to the microarray chip(s).Examples of such nucleosides include adenosine, guanosine, cytidine,thymidine and uridine. Any nucleotides can be attached to the microarraychip(s). Examples of such nucleotides include AMP, GMP, CMP, UMP, ADP,GDP, CDP, UDP, ATP, GTP, CTP, UTP, dAMP, dGMP, dCMP, dTMP, dADP, dGDP,dCDP, dTDP, dATP, dGTP, dCTP and dTTP.

[0083] Any vitamins can be attached to the microarray chip(s). Forexample, water-soluble vitamins such as thiamine, riboflavin, nicotinicacid, pantothenic acid, pyridoxine, biotin, folate, vitamin B₁₂ andascorbic acid can be attached. Similarly, fat-soluble vitamins such asvitamin A, vitamin D, vitamin E, and vitamin K can be attached.

[0084] Any monosaccharides, whether D- or L-monosaccharides and whetheraldoses or ketoses, can be attached to the microarray chip(s). Examplesof monosaccharides include triose such as glyceraldehyde, tetroses suchas erythrose and threose, pentoses such as ribose, arabinose, xylose,lyxose and ribulose, hexoses such as allose, altrose, glucose, mannose,gulose, idose, galactose, talose and fructose and heptose such assedoheptulose.

[0085] Any lipids can be attached to the microarray chip(s). Examples oflipids include triacylglycerols such as tristearin, tripalmitin andtriolein, waxes, phosphoglycerides such as phosphatidylethanolamine,phosphatidylcholine, phosphatidylserine, phosphatidylinositol andcardiolipin, sphingolipids such as sphingomyelin, cerebrosides andgangliosides, sterols such as cholesterol and stigmasterol and sterolfatty acid esters. The fatty acids can be saturated fatty acids such aslauric acid, myristic acid, palmitic acid, stearic acid, arachidic acidand lignoceric acid, or can be unsaturated fatty acids such aspalmitoleic acid, oleic acid, linoleic acid, linolenic acid andarachidonic acid.

[0086] In a specific embodiment, at least two of the microarray chipscan have attached thereto a plurality of moieties. However, any numberor percentage of the microarray chips, e.g., 50% of the microarraychips, can have attached thereto a plurality of moieties. Preferably,each of the microarray chips has attached thereto a plurality ofmoieties. The microarray chips can have attached thereto same type ordifferent type of moieties. In another specific embodiment, at least oneof the microlocations can comprise a temperature controller. However,any number or percentage of the microlocations, e.g., 50% of themicrolocations, can comprise a temperature controller. preferably, eachof the microlocations comprises a temperature controller. Morepreferably, each of the microlocations comprises a microarray chip and atemperature controller. Some, e.g., 50% of the temperature controllers,can be individually controllable. Preferably, each of the temperaturecontroller is individually controllable.

[0087] Any suitable temperature controller can be used in the presentdevice. For example, a resistive heater, a bidirectional semiconductortemperature controller, a ceramic heater or an infrared heater can beused.

[0088] The substrate in the present device can be an unitary unit.Alternatively, the substrate can be an assembled unit, which can bedisassembled into at least two parts.

[0089] C. Detecting Methods

[0090] In another aspect, the invention provides a method for detectinginteraction between a test moiety and a plurality of target moieties,which method comprises: a) providing an integrated microarray device,which device comprises a substrate comprising a plurality of distinctmicrolocations and a plurality of microarray chips, wherein the numberof said microlocations equals to or is more than the number of saidmicroarray chips, and a plurality of target moieties attached to saidmicroarray chips; b) contacting a test moiety with said plurality oftarget moieties provided in step a); and c) detecting interactionbetween said test moiety and said plurality of target moieties. Thepresent methods can be used in any suitable fields including prognosis,diagnosis, drug screening, environmental monitoring, etc.

[0091] Any suitable integrated microarray device, including the devicesdescribed in the above Section B, can be used in the present method. Ina specific embodiment, the integrated microarray device comprises asubstrate comprising a plurality of distinct microlocations and each ofthe microlocations comprises a microarray chip and a temperaturecontroller.

[0092] The present methods can be used to detect any interaction(s)among moieties selected from the group consisting of a cell, a cellularorganelle, a virus, a molecule and an aggregate or complex thereof. Forexample, the present methods can be used to detect interactions betweenor among macromolecules, such as DNA-DNA, DNA-RNA, RNA-RNA, DNA-protein,RNA-protein and protein-protein, etc., interactions. The present methodscan also be used to detect macromolecule-small molecule or smallmolecule-small molecule interactions. The present methods can also beused to detect more complex interactions including interactions amongmore than two moieties. When DNA-DNA, DNA-RNA, RNA-RNA interactions areto be detected, the contacting, i.e., hybridizing, step, can beconducted under suitable condition, e.g., under low, middle or highstringency.

[0093] The interaction between said test moiety and said plurality oftarget moieties can be detected by any suitable methods. For example,the test moiety and/or target moieties can be labeled to facilitatedetection. Any suitable label can be used. Exemplary labels include aradioactive, a fluorescent, a chemical, an enzymatic, a luminescent anda FRET (fluorescence resonance energy transfer) label. The luminescentlabel can be a chemiluminescent label or a bioluminescent label. Thelabels can be attached or conjugated, directly or indirectly, to thetest moiety alone, the target moiety alone, or on both. The read-out canbe a positive or a negative signal. Any suitable assay formats,including sandwich or competitive formats, can be used.

[0094] In a preferred embodiment, the present methods are used to detectinteraction between or among a test moiety and a plurality of genes,gene fragments or their encoded products. More preferably, the pluralityof target genes, gene fragments or their encoded products are involvedin a biological pathway, belong to a group of proteins with identical orsimilar biological function, expressed in a stage of cell cycle,expressed in a cell type, expressed in a tissue type, expressed in anorgan type, expressed in a developmental stage, proteins whoseexpression and/or activity is altered in a disease or disorder type orstage, or proteins whose expression and/or activity is altered by drugor other treatments.

[0095] The present methods can be used in detecting interaction betweenor among a single test moiety or substance and a plurality of targetmoieties. Preferably, the present methods are used in high-throughputmode, i.e., in detecting interaction between or among a plurality oftest moieties or substances and a plurality of target moieties. Theinteraction between a plurality of test moieties or substances and aplurality of target moieties can be detected simultaneously orsequentially.

[0096] D. Description of Exemplary Devices

[0097]FIG. 1 is the top-view schematic illustration of an exemplaryintegrated microarray device. This device includes a substrate 1.Substrate 1 can be made of plastics, glass, silicon, ceramics etc., andcan be porous or nonporous, rigid or flexible.

[0098] Multiple reaction wells 2 are fabricated on the substrate 1 byappropriate methods such as etching. Then every reaction well isintroduced with a microarray chip 3. The number of reaction wells anddistance between different wells can be modified according to thepractical need. If possible, it is recommended that the parameters (suchas the number of reaction wells or distance between or among differentwells) of wells be identical to a standard plate, such as standard96-well plate, 384-well plate or 1536-well plate, to facilitateautomated manipulation (such as sample handling or washing) by robotics.In the example shown in FIG. 1, the dimensional parameter of themicroarray device is identical to a standard 96-well plate. That is,there are 96 reaction wells 2 on the substrate 1, and the distance fromone well to the adjacent well is 9 mm, identical to the distance betweenadjacent wells on a standard 96-well plate.

[0099] The three dimensional schematic illustration of a well unit ofthe microarray device is shown in FIG. 2 in which a reaction well 2 andattached microarray chip 3 are drawn. The shape of the top port of thereaction well is quadrate. The diameter of its circumcircle should besmaller than or equal to that of a standard 96-well plate. And the shapeof microarray chip 3 which is placed in the reaction well 2 is quadratetoo. In this preferred embodiment, the quadrate shape of reaction well 2and microarray chip 3 ensures the correct positioning orientation ofmicroarray chip 3. Skilled artisans will understand that the shape isnot limited to quadrate. Other shapes such as orbicular can also beadopted to shape the reaction well 2 and microarray chip 3. Formicroarray chip 3, the surface on which probes are immobilized may faceup (FIG. 2A) or face down (FIG. 2B). The bottom of reaction well 2 maybe sealed and reagents (e.g., hybridization reagents or washingreagents) could then be added in or moved out from top (FIG. 2A).Alternatively, the bottom of the device can be designed to be partiallyopen, namely at least one microfluidic channel will be fabricated on thebottom to facilitate the addition or removal of reagents (hybridizationreagents or washing reagents) from the bottom (FIG. 2B). Reaction well 2may be fabricated as a whole device, or it may include at least twodissembled parts. For example, if needed, the bottom of the reactionwell can be pulled down to undergo the subsequent detection. The depthof reaction well 2 can be modified according to the thickness ofmicroarray chip 3 and the reaction volume can be varied from severalhundreds micrometers to several centimeters.

[0100] When the present microarray device is applied to detectingbiological or pharmaceutical samples, probes can be divided intodifferent groups according to their properties such as number of basesor sequence of probes. Probes from the same group are then immobilizedon the same microarray chip 3 in a reaction well 2. Probes can be cDNA,oligonucleotides, antigens or antibodies, receptors, polypeptides, cellsor tissues. The substrate of microarray chip 3 can be silicon, glass ornylon membrane etc. Immunobilization methods for probes can beabsorption, covalent binding, entrapment etc. (Beattie et al., MolecularBiotechnology, 4:213-225, (1995); and Subramanian et al., Enzyme &Microbial Technol, 24:26-34, (1999)).

[0101] In many cases such as diagnosis of one kind of disease, screeningone kind of drug or researching some specific genes' functions,microarray with high density is not absolutely necessary. Microarraychip 3 of the present device may be of low density microarray chip onwhich only several tens or several hundreds probes are immobilized. Thecorresponding fabrication costs can be decreased a lot by using lowdensity microarray chips. On the other hand, the microarray device ofthis invention includes multiple units (for example, the number of unitsmay be 96, 384 or 1536). Though the number of probes in every reactionwell is not high, the number of probes in all these reaction wellstogether may range from several thousands to several hundreds thousandsto achieve high-throughput analysis and also provide middle sizeddensity.

[0102] To control temperature in every reaction well 2, illustrated byFIG. 2, a temperature controller 6 is attached to every reaction well 2.FIG. 3 illustrates an exemplary connection between different temperaturecontrollers 6. There are two lines 9 and 9′ stretching from everytemperature controller 6 connected to anode and cathode of power supplyrespectively. Individual control of temperature of different reactionwells 2 may be achieved by addressable activation/inactivation ofdifferent temperature controllers 6.

[0103] Temperature controller 6 may simply be a resistor applied to heatreaction well 2. It may be attached to the bottom of reaction well 2. Ifsubstrate is made of silicon, microfabrication technology may be appliedto etch the opposite face of reaction well 2, then deposit a layer ofmetal (such as copper) on silicon to fabricate temperature controller 6.And the bottom of reaction well 2 is fabricated as thin as possible tofacilitate heat transfer between temperature controller 6 and microarraychip 3 in the reaction well 2. Alternatively, temperature controller 6may be a bidirectional semiconductor temperature controller. On the onehand, this bidirectional semiconductor temperature controller may heatreaction well 2; on the other hand, it may cool reaction well 2 when itstemperature is higher than environmental temperature (such as 50° C.).This bidirectional semiconductor temperature controller may be attachedto the bottom of reaction well 2. Temperature controller 6 may also beput into reaction well 2 by the way illustrated by FIG. 2B. Temperaturecontroller 6 may be bond to microarray chip 3 by mechanical rabbetjoint. Alternatively, the binding may be achieved by introducing a layerof liquid, which would not take part in reaction or evaporate during thereaction. The binding force is surface tension between the surface ofthis liquid and that of the temperature controller 6. Moreover, theintroduced liquid would also facilitate the heat transfer.

[0104] Skilled artisans will understand that any kinds of temperaturecontrollers, not just limited to resistors or bidirectionalsemiconductor temperature controllers, can be applied to temperaturecontroller 6 of this invention. For example, ceramics heater can beapplied to temperature controller 6 by attaching it directly to thebottom of reaction well 2. Alternatively, infrared heating can beapplied by using the non-contact infrared waves. The connecting waybetween temperature controller 6 and computer to achieve addressablecontrol of temperature controller 6 is not limited to the way mentionedabove. Any appropriate ways for temperature control can be applied.

[0105] In the preferred embodiment of the device in this inventionillustrated by FIG. 1 and FIG. 2, through holes fabricated on theinsulation wall between every reaction well, different reaction wellsare connected to each other by thin girders to facilitate heatinsulation between different reaction well 2. The size of the holeshould be as large as possible as long as the tightness of the system isenough. For example, if the substrate is made of plastics, the size ofevery pore may be 3×2 millimeters. According to different materialsused, different fabrication methods may be applied, such as laserablation (Simpson et al., Proc. Natl. Acad. Sci. USA, 95:2256-2261(1998)), molding (Becker et al., Sensors Update, 3:208-238 (1998); andDelamarche et al., J. Am. Chem. Soc., 120:500-508 (1998)), and embossing(Kopp et al., Current Opinion in Chemical Biology, 1:410-419 (1997)).

[0106] When the present microarray device is applied to biochemicalreactions, a cover-slip may be used to cover the sample solution afterthe solution is added to microarray chip 3 in the reaction well 2. Itwill help avoiding evaporation of the sample. And the size of cover-slipis flexible according to microarray chip's size (no larger than the areaof microarray chip 3). Alternatively, as illustrated by FIG. 2, highboiling point hydrophobic organic reagents (such as mineral oil) can beapplied to block the reaction system. The reagent volume should bedecided by the sample volume and the area of microarray chip. Asillustrated in FIG. 2B, when microarray chip 3 is placed in a face-downposition into the reaction well, hydrophobic and bio-compatible liquid10 can be added to fill the reaction well 2. And this liquid's specificgravity and boiling point should be higher than water to allow samplefloating above the liquid to interact with probes attached on themicroarray chip 3. After reaction, liquid 10 can be drawn out throughmicrofluidic channel fabricated on the bottom of reaction well 2, andwashing solution can be added in.

[0107] The detection of reaction results can be completed by a chargecoupled device (CCD) or isotope imager. It should be decided upon by thelabeling methods applied to samples. Integrated microarray device can beplaced on the microscope stage, which can move with predetermineddistance steadily. The detector can detect one microarray chip 3 at onetime, then the motorized can move to the position of next reaction wellto be scanned. Such detection devices are cheap, effective, simple andeasy to use so they are possible to be applied in small hospitals orlaboratories.

REFERENCES CITED

[0108] Beattie W. G et al., “Hybridization of DNA targets toglass-tethered oligonucleotide probes”, Molecular Biotechnology 4:213-225, 1995

[0109] Becker H. et al., “Integrated capillary electrophoresis forchemical analysis”, in Baltes H. et al. (Eds), Sensors Update, Vol.3,VCH Weiheim 208-238, 1998

[0110] Delamarche E. et al., “Microfluidic networks for chemicalpatterning of substrate: Design and application to bioassays”, J. Am.Chem. Soc. 120: 500-508, 1998

[0111] Fodor S. P. A. et al., “Light-directed spatially addressableparallel chemical synthesis”, Science 251: 767-773, 1991

[0112] Hacia J. G et al., “Detection of heterozygous mutations in BRCA1using high density oligonucleotide arrays and two-colour fluorescenceanalysis”, Nature Genetics 14: 441-447, 1996;

[0113] Heller R. A. et al., “Discovery and analysis of inflammatorydisease-related genes using cDNA microarrays”, Proc. Natl. Acad. Sci.USA 94: 2150-2155, 1997

[0114] Kopp M. U. et al., “Developments in technology and applicationsof Microsystems”, Current Opinion in Chemical Biology 1: 410-419, 1997,

[0115] Simpson P. C. et al., “High-throughput genetic analysis usingmicrofabricated 96-sample capillary array electrophoresis microplates”,Proc. Natl. Acad. Sci. USA 95: 2256-2261, 1998

[0116] Subramanian A. et al., “Comparison of techniques for enzymeimmobilization on silicon supports”, Enzyme & Microbial Technol. 24:26-34, 1999.

[0117] The above examples are included for illustrative purposes onlyand are not intended to limit the scope of the invention. Manyvariations to those described above are possible. Since modificationsand variations to the examples described above will be apparent to thoseof skill in this art, it is intended that this invention be limited onlyby the scope of the appended claims.

What is claimed is:
 1. An integrated microarray device, which devicecomprises a substrate comprising a plurality of distinct microlocationsand a plurality of microarray chips, wherein the number of saidmicrolocations equals to or is more than the number of said microarraychips.
 2. The device of claim 1, wherein the substrate comprisessilicon, plastic, glass, ceramic, rubber, polymer. or a compositethereof.
 3. The device of claim 2, wherein the silicon is silicondioxide or silicon nitride.
 4. The device of claim 1, wherein thesubstrate comprises a surface that is hydrophobic or hydrophilic.
 5. Thedevice of claim 1, wherein the substrate comprises a surface that isporous or nonporous.
 6. The device of claim 1, wherein themicrolocations and/or the microarray chips are fabricated on thesubstrate.
 7. The device of claim 1, which comprises (12)_(n) number ofmicrolocations, wherein n is an integer that is at least
 1. 8. Thedevice of claim 1, wherein the microlocations are evenly or unevenlydistributed on the substrate.
 9. The device of claim 1, wherein thenumber microlocations and the distance among the microlocationscorrespond to a standard microtiter plate.
 10. The device of claim 1,wherein the microlocations are in a well format or a thermally insulatedflat surface format.
 11. The device of claim 10, which comprises(12)_(n) number of wells, wherein n is an integer that is at least 1.12. The device of claim 10, which comprises 96, 384 or 1,536 wells. 13.The device of claim 10, wherein the wells have a geometry selected fromthe group consisting of circle, oval, square, rectangle, triangle andother irregular shape(s).
 14. The device of claim 10, wherein the wellshave identical or different shapes.
 15. The device of claim 1, whereinat least one of the microlocations is in fluid contact with a fluidsource or fluid passage outside the device.
 16. The device of claim 1,wherein all of the microlocations are in fluid contact with a fluidsource or fluid passage outside the device.
 17. The device of claim 1,wherein at least two of the microlocations are in fluid contact witheach other.
 18. The device of claim 1, wherein all of the microlocationsare in fluid contact with each other.
 19. The device of claim 1, whereinat least one of the microlocations is thermally insulated.
 20. Thedevice of claim 1, wherein all of the microlocations are thermallyinsulated.
 21. The device of claim 10, wherein at least one of the wellsis thermally insulated.
 22. The device of claim 10, wherein all of thewells are thermally insulated.
 23. The device of claim 19, wherein themicrolocation(s) is thermally insulated by inert gas.
 24. The device ofclaim 23, wherein the inert gas is air.
 25. The device of claim 22,wherein all of the wells are connected to each other by thin girders andthermally insulated by the air contained between the walls of theadjacent wells. 26.- The device of claim 1, wherein each of themicrolocations comprises a microarray chip.
 27. The device of claim 1,wherein the microarray chips have identical or different densities. 28.The device of claim 1, wherein the microarray chips have a density of(100)_(n) spots/cm², wherein n is an integer that is at least
 1. 29. Thedevice of claim 1, wherein at least one of the microarray chips has adensity that is less than or equals to 400 spots/cm².
 30. The device ofclaim 1, wherein all of the microarray chips have a density that is lessthan or equals to 400 spots/cm².
 31. The device of claim 1, wherein atleast one of the microarray chips has attached thereto a plurality ofmoieties.
 32. The device of claim 31, wherein the microarray chip(s) hasattached thereto a plurality of moieties on facing up or down direction.33. The device of claim 31, wherein each of the moieties is selectedfrom the group consisting of a cell, a cellular organelle, a virus, amolecule and an aggregate or complex thereof.
 34. The device of claim33, wherein the cell is selected from the group consisting of an animalcell, a plant cell, a fungus cell, a bacterium cell, a recombinant celland a cultured cell.
 35. The device of claim 33, wherein the cellularorganelle is selected from the group consisting of a nuclei, amitochondrion, a chloroplast, a ribosome, an ER, a Golgi apparatus, alysosome, a proteasome, a secretory vesicle, a vacuole and a microsome.36. The device of claim 33, wherein the molecule is selected from thegroup consisting of an inorganic molecule, an organic molecule and acomplex thereof.
 37. The device of claim 36, wherein the inorganicmolecule is an ion selected from the group consisting of a sodium, apotassium, a magnesium, a calcium, a chlorine, an iron, a copper, azinc, a manganese, a cobalt, an iodine, a molybdenum, a vanadium, anickel, a chromium, a fluorine, a silicon, a tin, a boron and an arsenicion.
 38. The device of claim 36, wherein the organic molecule isselected from the group consisting of an amino acid, a peptide, aprotein, a nucleoside, a nucleotide, an oligonucleotide, a nucleic acid,a vitamin, a monosaccharide, an oligosaccharide, a carbohydrate, a lipidand a complex thereof.
 39. The device of claim 1, wherein at least twoof the microarray chips have attached thereto a plurality of moieties.40. The device of claim 39, wherein each of the microarray chips hasattached thereto same type or different type of moieties.
 41. The deviceof claim 1, wherein each of the microarray chips has attached thereto aplurality of moieties.
 42. The device of claim 1, wherein at least oneof the microlocations comprises a temperature controller.
 43. The deviceof claim 42, wherein each of the microlocations comprises a temperaturecontroller.
 44. The device of claim 42, wherein each of the temperaturecontroller is individually controllable.
 45. The device of claim 42,wherein the temperature controller is selected from the group consistingof a resistive heater, a bidirectional semiconductor temperaturecontroller, a ceramic heater and an infrared heater.
 46. The device ofclaim 1, wherein the substrate is an unitary unit.
 47. The device ofclaim 1, wherein the substrate is an assembled unit, which can bedisassembled into at least two parts.
 48. A method for detectinginteraction between a test moiety and a plurality of target moieties,which method comprises: a) providing an integrated microarray device,which device comprises a substrate comprising a plurality of distinctmicrolocations and a plurality of microarray chips, wherein the numberof said microlocations equals to or is more than the number of saidmicroarray chips, and a plurality of target moieties attached to saidmicroarray chips; b) contacting a test moiety with said plurality oftarget moieties provided in step a); and c) detecting interactionbetween said test moiety and said plurality of target moieties.
 49. Thedevice of claim 48, wherein the integrated microarray device comprises asubstrate comprising a plurality of distinct microlocations and each ofthe microlocations comprises a microarray chip and a temperaturecontroller.
 50. The device of claim 48, wherein the interaction beingdetected are interaction(s) among moieties selected from the groupconsisting of a cell, a cellular organelle, a virus, a molecule and anaggregate or complex thereof.
 51. The device of claim 48, wherein theplurality of target moieties is a plurality of genes, gene fragments ortheir encoded products.
 52. The device of claim 51, wherein theplurality of genes, gene fragments or their encoded products areinvolved in a biological pathway, belong to a group of proteins withidentical or similar biological function, expressed in a stage of cellcycle, expressed in a cell type, expressed in a tissue type, expressedin an organ type, expressed in a developmental stage, proteins whoseexpression and/or activity is altered in a disease or disorder type orstage, or proteins whose expression and/or activity is altered by drugor other treatments.
 53. The device of claim 48, wherein interactionbetween a plurality of target moieties and a plurality of targetmoieties are detected.
 54. The device of claim 48, wherein interactionbetween a plurality of target moieties and a plurality of targetmoieties are detected simultaneously or sequentially.